State regulators say Minnesota must crack down on decrepit septic systems and livestock waste if it hopes to rescue its most polluted major river — the Minnesota — from E. coli contamination so severe that long stretches of it are unsafe for swimming.

Cleaning up bacterial pollution will cost $4 million to $10 million over two decades, according to a new plan from the Minnesota Pollution Control Agency (MPCA) that signals the state’s latest effort to solve a decades-old pollution problem in the river.

State regulators first identified the Minnesota River as “impaired,” or polluted under federal water-quality rules, in 1994 because of its high levels of nitrogen, phosphorus, sediment and other contaminants.

The agency’s new draft report zeros in on bacterial pollution in the main stem of the Minnesota and pinpoints the sources with greater specificity than previous studies. But the findings come as no surprise, given that the Minnesota cuts through the heart of the state’s farm country, with hundreds of feedlots and thousands of acres of intensively farmed corn and soybeans.

“We have an agricultural economy in that basin, and that’s also a really important part of Minnesota,” said Bonnie Keeler, an environmental and water policy professor at the University of Minnesota’s Humphrey School. “It is an equation I don’t think anyone has solved.”

A draft of the so-called total maximum daily load (TMDL) report is open for public comment until March 6.

E. coli is a type of fecal coliform bacteria found in human sewage and animal manure. The standard for aquatic life and recreational waters like the Minnesota River is 126 organisms per 100 millimeters of water. Lakes and rivers are listed as “impaired” if they exceed that standard, and the federal Clean Water Act requires states to perform TMDL studies on those waters to specify sources, target levels and solutions.

The new report focuses on five stretches of the Minnesota River, four of which have been listed as impaired for E. coli since 1994.

Asked why it took more than two decades to produce the latest plan, MPCA staff said the agency had to tackle upstream tributaries first, particularly the ones violating water quality standards more often. And it shifted to looking at entire watersheds about a decade ago.

Such lags are not uncommon, according to officials with the U.S. Environmental Protection Agency (EPA).

“That’s probably getting a little bit longer than most,” said Dave Werbach, the EPA’s regional TMDL coordinator. The federal Clean Water Act requires the water quality improvement plans, he said, but doesn’t set deadlines.

The levels of E. coli contamination in the Minnesota River are described as low to moderate compared with the levels found in the streams and tributaries that feed it. The levels would probably be higher if the river didn’t have such a high volume of water flowing through it, diluting concentrations, said Scott MacLean, a watershed supervisor in Mankato for the MPCA.

“To be honest when I first saw the data I was a little surprised,” MacLean said.

The report also estimates that 10 to 18 percent of the septic systems in the study area are so bad they’re considered an imminent public health threat.

Don Arnosti, executive director of the Izaak Walton League’s Minnesota division, said it’s shocking that 40 years after the Clean Water Act, the state is still wrestling with obsolete septic systems.

“That’s illegal,” Arnosti said.

‘This isn’t rocket science’

The Minnesota River has proved a vexing environmental challenge. It’s a top source of pollution for the Mississippi, which it joins in St. Paul. Hundreds of millions of dollars have been spent on the Minnesota River watershed since 1992, when Gov. Arne Carlson set the goal of making it “fishable and swimmable in 10 years.”

Yet a major assessment in 2017 deemed the river still “unhealthy.”

Now, the MPCA is calling for reducing E. coli levels by 19 percent in some stretches and up to 60 percent in others, namely the downstream stretch from Cherry Creek, north of St. Peter, to High Island Creek near Arlington.

To tackle the human waste, the report recommends more frequent inspections of private septic systems and replacement of those that are out of compliance. At issue are an unspecified number of septic systems considered an “imminent public health threat.” Those include rudimentary straight-pipe systems that deliver untreated waste straight into water or ground surfaces.

The plan specifically targets so-called unpermitted livestock operations — typically, farms with fewer than 1,000 animal “units” that don’t require a waste permit from the MPCA. Larger, permitted feedlots aren’t considered a significant source of pollution, it says, because they are required to disinfect their wastewater to reduce fecal coliform concentrations.

There are more than 600 unpermitted animal feedlots — mostly holding hogs and cattle — in the study area, primarily in the stretch from the Blue Earth River to Cherry Creek near St. Peter. The smaller, unpermitted operations are typically part of county feedlot programs.

Citizen enforcement?

Bobby King, policy program director with the Land Stewardship Project, which opposes large animal feedlots, questioned why the plan assumes that large, permitted feedlots aren’t a problem.

“It just defies common sense,” King said.

King accused the MPCA of not having “the courage to acknowledge the problem is large factory farms.”

The MPCA’s MacLean said permitted feedlots get regular inspections: “By and large, we don’t see problems on site with those facilities,” he said.

MacLean acknowledged that problems are more likely to happen when manure leaves a farm and is applied on fields.

While the plan doesn’t give an exact number of badly deficient septic systems, the scale of its findings should trouble state regulators, Arnosti said.

“Maybe we need some citizen enforcement here, because we’re not getting government enforcement,” he said.

In an interview, environmental staff at Blue Earth County, for example, said they’ve been busy replacing septic systems but estimated that the part of the county in the study area still has roughly 125 straight-pipe systems.

Statewide, there are an estimated 25,000 worst-case septic systems. That’s down from more than 50,000 a decade ago, but it’s still a problematic number.

Said the MPCA’s MacLean: “I think we’re chipping away at this problem little by little.”

Jennifer Bjorhus is a reporter covering the environment for the Star Tribune. She was a business reporter for much of her career but in recent years focused on criminal justice issues, including police use of force and responses to sexual assault.